Although the court
of the Yuan Empire adopted
Tibetan Buddhism as the official
religion, the majority of the
ordinary
Mongols, especially those who
continued living in Mongolia proper,
remained Shamanists. After the
decline of the
Yuan Dynasty,
Shamanism once again became the
dominant religion. To varying
degrees, political and economic
relations with
Muslim nations such as
Mughalistan and the Uyghurs
continued.

The
Muslim Kazakhs began to settle
in
Jungaria and
Altai regions since the late
nineteenth century. The majority of
these Kazakhs were the Kerei and
Naiman clans, many of them escaping
the persecution of the Czarist
Russia. When independent
Bogdo
Khan Mongolia was
established on 29 December 1911, the
Kazakhs in Xinjian and Altai regions
sought patronage of the restored
Khanate. The Government of
Bogdo Khan admitted them and
settled them in the western region
of the Mongolia's Kobdo territory.

Bayan-Ölgii aimag
was established as part of the
administrative reforms of the
Mongolian People's Republic in
1940. Islam is freely practised in
the country since Mongolia became a
democracy in 1990.